PDBe 1nt1

X-ray diffraction
2Å resolution

thrombin in complex with selective macrocyclic inhibitor


Function and Biology Details

Reaction catalysed:
Selective cleavage of Arg-|-Gly bonds in fibrinogen to form fibrin and release fibrinopeptides A and B. 
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Hirudin-2 Chain: H
Molecule details ›
Chain: H
Length: 11 amino acids
Theoretical weight: 1.38 KDa
Source organism: Hirudo medicinalis
Expression system: Not provided
  • Canonical: P28504 (Residues: 55-65; Coverage: 17%)
Thrombin heavy chain Chain: A
Molecule details ›
Chain: A
Length: 287 amino acids
Theoretical weight: 33.08 KDa
Source organism: Homo sapiens
  • Canonical: P00734 (Residues: 335-621; Coverage: 48%)
Gene name: F2
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2
Unit cell:
a: 71.1Å b: 72.1Å c: 73.2Å
α: 90° β: 100.9° γ: 90°
R R work R free
0.191 0.19 not available
Expression system: Not provided